Experiment set3IT080 for Pseudomonas sp. RS175

Compare to:

4-Hydroxybenzoic Acid carbon source 2.5 mM

Group: carbon source
Media: MME_noCarbon + 4-Hydroxybenzoic Acid (2.5 mM), pH=7
Culturing: Pseudomonas_RS175_ML2, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Joshua Elmore on 1-July-22
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 10 mM Ammonium chloride, 0.41 mM Magnesium Sulfate Heptahydrate, 0.07 mM Calcium chloride dihydrate, MME Trace Minerals (0.5 mg/L EDTA tetrasodium tetrahydrate salt, 2 mg/L Ferric chloride, 0.05 mg/L Boric Acid, 0.05 mg/L Zinc chloride, 0.03 mg/L copper (II) chloride dihydrate, 0.05 mg/L Manganese (II) chloride tetrahydrate, 0.05 mg/L Diammonium molybdate, 0.05 mg/L Cobalt chloride hexahydrate, 0.05 mg/L Nickel (II) chloride hexahydrate)

Specific Phenotypes

For 38 genes in this experiment

For carbon source 4-Hydroxybenzoic Acid in Pseudomonas sp. RS175

For carbon source 4-Hydroxybenzoic Acid across organisms

SEED Subsystems

Subsystem #Specific
Oxidative stress 3
ATP-dependent RNA helicases, bacterial 1
Arginine and Ornithine Degradation 1
Bacterial Chemotaxis 1
Biotin biosynthesis 1
Copper homeostasis: copper tolerance 1
DNA-binding regulatory proteins, strays 1
Histidine Degradation 1
Lysine Biosynthesis DAP Pathway 1
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria 1
Peptidoglycan Biosynthesis 1
Phenylalanine and Tyrosine Branches from Chorismate 1
Phosphate metabolism 1
Polyamine Metabolism 1
Proteasome bacterial 1
Proteolysis in bacteria, ATP-dependent 1
Thioredoxin-disulfide reductase 1
n-Phenylalkanoic acid degradation 1
p-Hydroxybenzoate degradation 1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
long-chain fatty acid activation 1 1 1
3-(4-hydroxyphenyl)pyruvate biosynthesis 1 1 1
cis-cyclopropane fatty acid (CFA) biosynthesis 1 1 1
L-phenylalanine biosynthesis III (cytosolic, plants) 2 2 1
γ-linolenate biosynthesis II (animals) 2 1 1
atromentin biosynthesis 2 1 1
linoleate biosynthesis II (animals) 2 1 1
L-tyrosine degradation II 2 1 1
sterculate biosynthesis 2 1 1
L-phenylalanine biosynthesis I 3 3 1
L-tyrosine biosynthesis I 3 3 1
L-phenylalanine degradation II (anaerobic) 3 2 1
3-methyl-branched fatty acid α-oxidation 6 3 2
L-tyrosine degradation IV (to 4-methylphenol) 3 1 1
alkane biosynthesis II 3 1 1
oleate biosynthesis I (plants) 3 1 1
L-histidine degradation I 4 4 1
L-phenylalanine biosynthesis II 4 3 1
L-tyrosine biosynthesis III 4 3 1
phytol degradation 4 3 1
L-phenylalanine degradation III 4 2 1
4-chlorobenzoate degradation 4 2 1
L-tyrosine biosynthesis II 4 2 1
L-tyrosine degradation III 4 2 1
wax esters biosynthesis II 4 1 1
phosphatidylcholine acyl editing 4 1 1
long chain fatty acid ester synthesis (engineered) 4 1 1
4-methylphenol degradation to protocatechuate 4 1 1
sporopollenin precursors biosynthesis 18 4 4
L-tyrosine degradation I 5 5 1
L-arginine degradation II (AST pathway) 5 5 1
L-histidine degradation II 5 5 1
octane oxidation 5 4 1
superpathway of L-phenylalanine and L-tyrosine biosynthesis 5 3 1
sphingosine and sphingosine-1-phosphate metabolism 10 4 2
superpathway of plastoquinol biosynthesis 5 2 1
4-coumarate degradation (aerobic) 5 2 1
4-hydroxybenzoate biosynthesis I (eukaryotes) 5 1 1
L-phenylalanine degradation VI (reductive Stickland reaction) 5 1 1
L-tyrosine degradation V (reductive Stickland reaction) 5 1 1
bisphenol A degradation 5 1 1
fatty acid salvage 6 6 1
stearate biosynthesis II (bacteria and plants) 6 5 1
stearate biosynthesis IV 6 4 1
L-histidine degradation III 6 4 1
6-gingerol analog biosynthesis (engineered) 6 3 1
peptidoglycan maturation (meso-diaminopimelate containing) 12 4 2
4-hydroxymandelate degradation 6 2 1
stearate biosynthesis I (animals) 6 1 1
capsaicin biosynthesis 7 4 1
spongiadioxin C biosynthesis 7 2 1
ceramide degradation by α-oxidation 7 2 1
icosapentaenoate biosynthesis III (8-desaturase, mammals) 7 1 1
arachidonate biosynthesis III (6-desaturase, mammals) 7 1 1
icosapentaenoate biosynthesis II (6-desaturase, mammals) 7 1 1
L-histidine degradation VI 8 7 1
2-deoxy-D-ribose degradation II 8 4 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
polybrominated dihydroxylated diphenyl ethers biosynthesis 8 2 1
superpathway of aromatic amino acid biosynthesis 18 18 2
L-lysine biosynthesis I 9 9 1
L-phenylalanine degradation IV (mammalian, via side chain) 9 5 1
L-histidine biosynthesis 10 10 1
superpathway of L-tyrosine biosynthesis 10 10 1
superpathway of L-phenylalanine biosynthesis 10 10 1
rosmarinic acid biosynthesis I 10 2 1
suberin monomers biosynthesis 20 3 2
superpathway of fatty acid biosynthesis II (plant) 43 38 4
toluene degradation III (aerobic) (via p-cresol) 11 7 1
(S)-reticuline biosynthesis I 11 1 1
tropane alkaloids biosynthesis 11 1 1
superpathway of rosmarinic acid biosynthesis 14 2 1
palmitate biosynthesis II (type II fatty acid synthase) 31 29 2
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis 16 3 1
cutin biosynthesis 16 1 1
peptidoglycan biosynthesis II (staphylococci) 17 12 1
peptidoglycan biosynthesis IV (Enterococcus faecium) 17 12 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 16 1
aspartate superpathway 25 22 1
superpathway of fatty acids biosynthesis (E. coli) 53 49 2
anaerobic aromatic compound degradation (Thauera aromatica) 27 4 1
palmitate biosynthesis III 29 28 1
superpathway of chorismate metabolism 59 43 2
superpathway of aerobic toluene degradation 30 11 1
oleate β-oxidation 35 30 1
superpathway of aromatic compound degradation via 3-oxoadipate 35 13 1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate 42 10 1
superpathway of histidine, purine, and pyrimidine biosynthesis 46 44 1
mycolate biosynthesis 205 20 3
superpathway of mycolate biosynthesis 239 21 3